Phylogeography of Orinus (Poaceae), a dominant grass genus on the Qinghai-Tibet Plateau

Abstract

To better understand the responses of arid-adapted, alpine plants to Quaternary climatic oscillations, we investigated the genetic variation and phylogeographic history of Orinus, an endemic genus of Poaceae comprising three species from the dry grasslands of the Qinghai-Tibet Plateau (QTP) in China. We measured the genetic variation of 476 individuals from 88 populations using three maternally inherited plastid DNA markers (matK, rbcL and psbA-trnH), the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS) and amplified fragment length polymorphisms (AFLPs). We found that the plastid DNA, nrITS and AFLPs show considerable, recent differentiation among the species. We detected 14 plastid haplotypes (H1-H14), of which only three were shared among all species, and 30 nrITS ribotypes (S1-S30), of which one (S10) was shared between two species, O. kokonoricus and O. intermedius, but absent in O. thoroldii. The nrITS types formed clades that were inconsistent with species boundaries. Based on these data, we propose and illustrate a complex hypothesis for the evolutionary history of Orinus involving lineage sorting and introgression, the latter of which may explain the shared S10 nrITS type. The AFLP results showed clades corresponding to current species delineation and suggest that lineage sorting in the genus is probably complete. We estimated the crown age of Orinus to be 2.85 (95% highest posterior density: 0.58-12.45) Mya (late Pliocene), and subsequent divergence occurred in the Quaternary. Early divergences were allopatric. More recently, Orinus probably underwent regional expansions corresponding to Quaternary climatic changes, especially glaciation, which is consistent with our divergence time estimates. These climatic changes could have facilitated the S10 event and other hybridization events. Our data also suggest that species of this small genus of grasses survived the Quaternary glacial period in the extremely adverse habitats of the QTP.

A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai–Tibet Plateau: Orinus (Poaceae)

“…In the present, the QTP exhibits substantial landscape heterogeneity; for example, its elevation range is from 3,000 to 5,000 m and represents a steep ecological gradient comprising diverse niches for a rich composition of species (Feng et al, ; Feng et al, ; Liu, Luo, Li, & Gao, ). With respect to environmental change, the QTP has undergone extreme ecological disturbances on an evolutionary timescale, especially rapid uplifts since the Miocene–Pliocene or Miocene–Quaternary epochs and subsequent climatic oscillations in the Quaternary (Liu, ; Liu, Gao, Chen, & Lu, ; Liu, Wang, Geng, et al, ; Liu, Wang, Wang, Hideaki, & Abbott, ; Liu et al, , ; Shi, ; Shi, Li, & Li, ; Wen, Zhang, Nie, Zhong, & Sun, ; Zheng & Nat, ). The biodiversity within the QTP is reflected within its flora, which harbors ca.…”

“…Within the alpine grasslands of the QTP, the dominant vascular plants are three endemic species comprising the entirety of the genus, Orinus Hitchcock (Figure ; Poaceae; Liu et al, ; Su, Wu, Li, & Liu, ). Orinus consists of clonal grasses and was established in 1933 by Hitchcock based on the type species O .…”

“…Nevertheless, O. intermedius appeared more likely to be an incompletely isolated sister of O . kokonoricus than a hybrid based on a population‐level phylogenetic study comprising chloroplast and nuclear ribosomal internal transcribed spacer (ITS; Liu et al, ). At present, the putative hybrid status of O. intermedius remains incompletely resolved.…”

“…Finally, Orinus possesses an extensive system of roots and rhizomes (Cai, ; Su et al, ; Su, Yue, & Liu, ) that limit soil loss within the wind‐swept alpine grasslands of the QTP (Figure ; Yang et al, ). Thus, the diversity and diversification of the genus can also yield insights into the timing, mechanisms, and ecological consequences of regional desertification (Guo et al, ; Han, Fang, & Berger, ; see also Liu et al, ).…”

Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations

“…Climatic oscillations and related changes in vegetation can be recognized in the period from 3.6 to 0.8 Ma (Naidina & Richards, ). Multiple studies have showed that the climate oscillations especially in the glaciation cycles of the Quaternary may have facilitated speciation, diversification, hybridization, and changes in the distribution of the global vegetation (Liu et al., ; Shahzad, Jia, Chen, Zeb, & Li, ; Yamamoto, Ohtani, Kurata, & Setoguchi, ).…”